6-10982740-T-C

Variant names:

• chr6-10982740-T-C
• rs3734398
• NM_017770.4:c.*1041A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_017770.4(ELOVL2):​c.*1041A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.425 in 152,032 control chromosomes in the GnomAD database, including 15,391 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.43 (15390 hom., cov: 32)
  • Exomes 𝑓: 0.50 (1 hom.)
• Consequence: ELOVL2 NM_017770.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.339
• Publications: 65 publications found

Genes affected

ELOVL2 (HGNC:14416): (ELOVL fatty acid elongase 2) Enables fatty acid elongase activity. Involved in fatty acid elongation, polyunsaturated fatty acid and very long-chain fatty acid biosynthetic process. Located in endoplasmic reticulum. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.884 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_017770.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ELOVL2	NM_017770.4	MANE Select	c.*1041A>G		3_prime_UTR	Exon 8 of 8	NP_060240.3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ELOVL2	ENST00000354666.4	TSL:1 MANE Select	c.*1041A>G		3_prime_UTR	Exon 8 of 8	ENSP00000346693.3	Q9NXB9
	ELOVL2	ENST00000912166.1		c.*1041A>G		3_prime_UTR	Exon 6 of 6	ENSP00000582225.1
	ELOVL2	ENST00000854792.1		c.*1041A>G		3_prime_UTR	Exon 5 of 5	ENSP00000524851.1

Frequencies

GnomAD3 genomes AF: 0.425 AC: 64577 AN: 151906 Hom.: 15372 Cov.: 32

Gnomad AFR AF: 0.251

Gnomad AMI AF: 0.313

Gnomad AMR AF: 0.581

Gnomad ASJ AF: 0.553

Gnomad EAS AF: 0.906

Gnomad SAS AF: 0.657

Gnomad FIN AF: 0.472

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.430

Gnomad OTH AF: 0.447

GnomAD4 exome AF: 0.500 AC: 4 AN: 8 Hom.: 1 Cov.: 0 AF XY: 0.250 AC XY: 1 AN XY: 4

African (AFR) AF: 0.500 AC: 1 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.500 AC: 3 AN: 6

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.425 AC: 64624 AN: 152024 Hom.: 15390 Cov.: 32 AF XY: 0.436 AC XY: 32383 AN XY: 74290

African (AFR) AF: 0.251 AC: 10408 AN: 41466

American (AMR) AF: 0.582 AC: 8874 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.553 AC: 1919 AN: 3470

East Asian (EAS) AF: 0.906 AC: 4684 AN: 5172

South Asian (SAS) AF: 0.656 AC: 3158 AN: 4816

European-Finnish (FIN) AF: 0.472 AC: 4982 AN: 10552

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.430 AC: 29221 AN: 67978

Other (OTH) AF: 0.452 AC: 955 AN: 2114

Alfa AF: 0.435 Hom.: 66429

Bravo AF: 0.425

Asia WGS AF: 0.731 AC: 2539 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.9
DANN	Benign	0.57
PhyloP100		0.34
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs3734398; hg19: chr6-10982973;